Basic Information
Locus ID:
Ag1G00373
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr1 | 42286030 | 42291218 | + | Ag1G00373 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 9.56 | 68,390.42 Da | 44.75 | 79.20 | -0.51 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd06171 | Sigma70_r4 | 528 | 586 | 4.64615E-13 | - |
| Pfam | PF04542 | Sigma-70 region 2 | 344 | 411 | 2.6E-17 | IPR007627 |
| Pfam | PF04545 | Sigma-70, region 4 | 534 | 586 | 1.1E-19 | IPR007630 |
| Pfam | PF04539 | Sigma-70 region 3 | 425 | 483 | 2.3E-12 | IPR007624 |
| SUPERFAMILY | SSF88659 | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 417 | 480 | 2.09E-10 | IPR013324 |
| SUPERFAMILY | SSF88946 | Sigma2 domain of RNA polymerase sigma factors | 271 | 414 | 8.95E-44 | IPR013325 |
| SUPERFAMILY | SSF88659 | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 505 | 596 | 3.55E-23 | IPR013324 |
| Gene3D | G3DSA:1.10.10.10 | - | 522 | 601 | 1.1E-27 | IPR036388 |
| Gene3D | G3DSA:1.10.601.10 | RNA Polymerase Primary Sigma Factor | 115 | 416 | 6.9E-39 | - |
| Gene3D | G3DSA:1.10.10.10 | - | 417 | 485 | 1.3E-11 | IPR036388 |
| TIGRFAM | TIGR02937 | sigma70-ECF: RNA polymerase sigma factor, sigma-70 family | 342 | 588 | 1.1E-29 | IPR014284 |
| PIRSF | PIRSF000767 | Sigma_factor_SigC | 1 | 488 | 1.8E-128 | IPR016262 |
| PIRSF | PIRSF000767 | Sigma_factor_SigC | 504 | 601 | 5.6E-44 | IPR016262 |
| ProSitePatterns | PS00716 | Sigma-70 factors family signature 2. | 559 | 585 | - | IPR000943 |
| PRINTS | PR00046 | Major sigma-70 factor signature | 538 | 550 | 2.1E-22 | IPR000943 |
| PRINTS | PR00046 | Major sigma-70 factor signature | 368 | 381 | 2.1E-22 | IPR000943 |
| PRINTS | PR00046 | Major sigma-70 factor signature | 559 | 574 | 2.1E-22 | IPR000943 |
| PRINTS | PR00046 | Major sigma-70 factor signature | 392 | 400 | 2.1E-22 | IPR000943 |
| PRINTS | PR00046 | Major sigma-70 factor signature | 574 | 585 | 2.1E-22 | IPR000943 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 230 | 269 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 255 | 269 | - | - |
Gene Ontology
Biological Process:
Molecular Function:
KEGG Pathway
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT1G08540.1 | RNApolymerase sigma subunit 2. Enodes a subunit of chloroplast RNA polymerase, confers the ability to recognize promoter sequences on the core enzyme. SIG1 is induced by red and blue light. | 0 |
| RefSeq | XP_017223885.1 | PREDICTED: RNA polymerase sigma factor sigB-like isoform X2 [Daucus carota subsp. sativus] | 0 |
| O22056 | RNA polymerase sigma factor sigB OS=Arabidopsis thaliana OX=3702 GN=SIGB PE=2 SV=2 | 0 | |
| TrEMBL | A0A175YEM7 | RNA polymerase sigma factor OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_029568 PE=3 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 13.30531 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 8.878018 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 10.909392 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 9.061304 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 8.781963 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 11.943707 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 6.826614 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 6.026274 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 37.546154 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 35.460793 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 41.078156 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 29.204401 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 30.954952 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 27.309429 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 18.075233 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 19.262934 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 20.051355 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 31.464298 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 41.297775 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 19.131741 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 17.289686 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 12.039102 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 16.396 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 20.550274 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 22.893974 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 36.938007 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 35.22303 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 37.887909 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 35.695377 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 5.345086 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 19.590797 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 14.307219 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 5.761292 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 8.176725 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 5.299649 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 2.969553 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 2.780492 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 2.311273 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 104.518074 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 51.888916 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 46.151791 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 1.191285 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 4.199479 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 12.668314 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 11.638838 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 4.104401 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 10.965532 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 30.489197 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 22.010406 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 24.875462 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 2 | jg1678, jg29090 |
| Aizoaceae | Mesembryanthemum crystallinum | 1 | gene_23115 |
| Amaranthaceae | Atriplex hortensis | 1 | Ah023418 |
| Amaranthaceae | Beta vulgaris | 1 | BVRB_7g172600 |
| Amaranthaceae | Salicornia bigelovii | 4 | Sbi_jg28739, Sbi_jg3221, Sbi_jg5769, Sbi_jg5770 |
| Amaranthaceae | Salicornia europaea | 1 | Seu_jg6705 |
| Amaranthaceae | Suaeda aralocaspica | 1 | GOSA_00000061 |
| Amaranthaceae | Suaeda glauca | 3 | Sgl11547, Sgl16923, Sgl17045 |
| Amaranthaceae | Chenopodium album | 3 | gene:ENSEOMG00000014613, gene:ENSEOMG00000035714 ... |
| Amaranthaceae | Chenopodium quinoa | 2 | CQ.Regalona.r1.1AG0008460, CQ.Regalona.r1.1BG0017410 |
| Anacardiaceae | Pistacia vera | 1 | pistato.v30094020 |
| Apiaceae | Apium graveolens | 3 | Ag10G00375, Ag1G00373, Ag5G01248 |
| Arecaceae | Cocos nucifera | 2 | COCNU_07G010890, COCNU_10G008190 |
| Arecaceae | Phoenix dactylifera | 1 | gene-LOC103718565 |
| Asparagaceae | Asparagus officinalis | 2 | AsparagusV1_01.1179.V1.1, AsparagusV1_08.65.V1.1 |
| Asteraceae | Flaveria trinervia | 2 | Ftri15G04390, Ftri18G30669 |
| Brassicaceae | Arabidopsis thaliana | 1 | AT1G08540.1 |
| Brassicaceae | Eutrema salsugineum | 1 | Thhalv10007187m.g.v1.0 |
| Brassicaceae | Schrenkiella parvula | 1 | Sp1g07200.v2.2 |
| Brassicaceae | Brassica nigra | 2 | BniB03g002780.2N, BniB04g031140.2N |
| Casuarinaceae | Casuarina equisetifolia | 1 | Ceq05G0169 |
| Casuarinaceae | Casuarina glauca | 1 | Cgl05G0176 |
| Cymodoceaceae | Cymodocea nodosa | 1 | gene.Cymno16g05810 |
| Dunaliellaceae | Dunaliella salina | 1 | Dusal.0049s00001.v1.0 |
| Hydrocharitaceae | Thalassia testudinum | 1 | gene.Thate05g11550 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 1 | nbisL1-mrna-8336 |
| Nitrariaceae | Nitraria sibirica | 1 | evm.TU.LG03.1931 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00016895, Pov_00016914 |
| Plumbaginaceae | Limonium bicolor | 2 | Lb1G03125, Lb2G11570 |
| Poaceae | Echinochloa crus-galli | 7 | AH01.4195, AH04.1190, BH01.4510, BH04.1150, CH01.4788 ... |
| Poaceae | Eleusine coracana subsp. coracana | 4 | gene-QOZ80_3AG0242670, gene-QOZ80_3BG0285540 ... |
| Poaceae | Hordeum vulgare | 2 | HORVU.MOREX.r3.4HG0374390.1, HORVU.MOREX.r3.4HG0388780.1 |
| Poaceae | Lolium multiflorum | 2 | gene-QYE76_066976, gene-QYE76_069038 |
| Poaceae | Oryza coarctata | 4 | Oco05G009380, Oco06G009720, Oco21G005050, Oco22G006200 |
| Poaceae | Oryza sativa | 2 | LOC_Os03g16430.1, LOC_Os11g26160.1 |
| Poaceae | Paspalum vaginatum | 2 | gene-BS78_01G403500, gene-BS78_05G127200 |
| Poaceae | Puccinellia tenuiflora | 3 | Pt_Chr0102274, Pt_Chr0102304, Pt_Chr0102962 |
| Poaceae | Sporobolus alterniflorus | 5 | Chr01G030860, Chr04G007610, Chr07G004010, Chr16G007370 ... |
| Poaceae | Thinopyrum elongatum | 2 | Tel4E01G303600, Tel4E01G368400 |
| Poaceae | Triticum dicoccoides | 4 | gene_TRIDC4AG013000, gene_TRIDC4AG022580 ... |
| Poaceae | Triticum aestivum | 6 | TraesCS4A02G095200.1, TraesCS4A02G157100.1 ... |
| Poaceae | Zea mays | 3 | Zm00001eb012130_P003, Zm00001eb169360_P001 ... |
| Poaceae | Zoysia japonica | 2 | nbis-gene-35996, nbis-gene-3768 |
| Poaceae | Zoysia macrostachya | 2 | Zma_g17867, Zma_g3938 |
| Portulacaceae | Portulaca oleracea | 2 | evm.TU.LG04.1713, evm.TU.LG10.1201 |
| Posidoniaceae | Posidonia oceanica | 1 | gene.Posoc07g00090 |
| Rhizophoraceae | Bruguiera sexangula | 1 | evm.TU.Scaffold_1_RagTag.486 |
| Rhizophoraceae | Carallia pectinifolia | 3 | nbisL1-mrna-3038, nbisL1-mrna-3130, nbisL1-mrna-7686 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-16022, nbisL1-mrna-19160 |
| Rhizophoraceae | Ceriops zippeliana | 2 | nbisL1-mrna-13930, nbisL1-mrna-5515 |
| Rhizophoraceae | Kandelia candel | 2 | evm.TU.utg000009l.241, evm.TU.utg000012l.300 |
| Rhizophoraceae | Kandelia obovata | 2 | Maker00005466, Maker00011153 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-12792, nbisL1-mrna-8495 |
| Rhizophoraceae | Rhizophora mangle | 2 | nbisL1-mrna-16408, nbisL1-mrna-630 |
| Salicaceae | Populus euphratica | 4 | populus_peu16193, populus_peu19289, populus_peu19290 ... |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132635716, gene-LOC132645103 |
| Solanaceae | Solanum chilense | 1 | SOLCI001247500 |
| Solanaceae | Solanum pennellii | 1 | gene-LOC107007105 |
| Tamaricaceae | Reaumuria soongarica | 3 | STRG.22652_chr10_-, STRG.22655_chr10_+, gene_2855 |
| Tamaricaceae | Tamarix chinensis | 1 | TC11G0235 |
| Zosteraceae | Zostera marina | 2 | Zosma05g01000.v3.1, Zosma06g01080.v3.1 |